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- PDB-8fg1: Human diaphanous inhibitory domain bound to diaphanous autoregula... -

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Basic information

Entry
Database: PDB / ID: 8fg1
TitleHuman diaphanous inhibitory domain bound to diaphanous autoregulatory domain
Components(Protein diaphanous homolog 1) x 2
KeywordsPROTEIN BINDING / inhibitory domain / autoregulatory domain
Function / homology
Function and homology information


protein localization to microtubule / cellular response to histamine / regulation of release of sequestered calcium ion into cytosol / regulation of microtubule-based process / RHOF GTPase cycle / RHOD GTPase cycle / microtubule organizing center / RHOB GTPase cycle / regulation of cytoskeleton organization / RHOC GTPase cycle ...protein localization to microtubule / cellular response to histamine / regulation of release of sequestered calcium ion into cytosol / regulation of microtubule-based process / RHOF GTPase cycle / RHOD GTPase cycle / microtubule organizing center / RHOB GTPase cycle / regulation of cytoskeleton organization / RHOC GTPase cycle / ERBB2 Regulates Cell Motility / ficolin-1-rich granule membrane / RHOA GTPase cycle / cytoskeleton organization / actin filament polymerization / secretory granule membrane / RHO GTPases Activate Formins / actin filament / sensory perception of sound / mitotic spindle / small GTPase binding / ruffle membrane / actin binding / regulation of cell shape / actin cytoskeleton organization / transmembrane transporter binding / signaling receptor binding / Neutrophil degranulation / RNA binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Formin Homology Region 1 / Diaphanous, GTPase-binding domain superfamily / Diaphanous autoregulatory (DAD) domain / Diaphanous autoregulatory domain (DAD) profile. / Formin, FH3 domain / Formin, GTPase-binding domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain ...Formin Homology Region 1 / Diaphanous, GTPase-binding domain superfamily / Diaphanous autoregulatory (DAD) domain / Diaphanous autoregulatory domain (DAD) profile. / Formin, FH3 domain / Formin, GTPase-binding domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain profile. / Formin, FH2 domain / Formin, FH2 domain superfamily / Formin Homology 2 Domain / Formin homology-2 (FH2) domain profile. / Formin Homology 2 Domain / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Protein diaphanous homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsRamirez, L.M.S. / Theophall, G. / Premo, A. / Manigrasso, M. / Yepuri, G. / Burz, D. / Ramasamy, R. / Schmidt, A.M. / Shekhtman, A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM085006 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)1R01DK122456 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)5P0HL146367 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Disruption of the productive encounter complex results in dysregulation of DIAPH1 activity.
Authors: Theophall, G.G. / Ramirez, L.M.S. / Premo, A. / Reverdatto, S. / Manigrasso, M.B. / Yepuri, G. / Burz, D.S. / Ramasamy, R. / Schmidt, A.M. / Shekhtman, A.
History
DepositionDec 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2May 15, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein diaphanous homolog 1
B: Protein diaphanous homolog 1


Theoretical massNumber of molelcules
Total (without water)32,2782
Polymers32,2782
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-7 kcal/mol
Surface area12440 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Protein diaphanous homolog 1 / Diaphanous-related formin-1 / DRF1


Mass: 29116.410 Da / Num. of mol.: 1 / Fragment: residues 142-380
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DIAPH1, DIAP1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60610
#2: Protein/peptide Protein diaphanous homolog 1 / Diaphanous-related formin-1 / DRF1


Mass: 3161.510 Da / Num. of mol.: 1 / Fragment: residues 1194-1222 / Mutation: M1199L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DIAPH1, DIAP1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60610

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
113isotropic13D CBCA(CO)NH
123isotropic13D HNCO
133isotropic13D HNCA
143isotropic13D HN(CA)CB
153isotropic13D HN(CO)CA
1143isotropic13D H(CCO)NH
191isotropic13D 1H-15N NOESY
182isotropic13D 1H-15N NOESY
175isotropic13D 1H-15N NOESY
161isotropic12D 1H-15N HSQC
1115isotropic12D 1H-15N HSQC
1104isotropic13D HNCA
1134isotropic13D HN(CA)CB
1124isotropic13D HN(CO)CA
1154isotropic13D HBHA(CO)NH
1164isotropic1H(CCH)-TOCSY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1300 uM [U-15N] Diaphanous inhibitory domain, 500 uM Diaphanous autoregulatory domain, 90% H2O/10% D2OSample was used to collect NOE distances for structure calculation15N_DID_DAD90% H2O/10% D2O
solution2300 uM [U-15N] Diaphanous inhibitory domain, 500 uM [U-13C] Diaphanous autoregulatory domain, 90% H2O/10% D2OSample was used to collect NOE distances for structure calculation15N_DID_13C_DAD90% H2O/10% D2O
solution3300 uM [U-100% 13C; U-100% 15N] Diaphanous inhibitory domain, 500 uM Diaphanous autoregulatory domain, 90% H2O/10% D2OSample was used to determine resonance assignment15N_13C_DID_DAD90% H2O/10% D2O
solution4300 uM Diaphanous inhibitory domain, 500 uM [U-100% 13C; U-100% 15N] Diaphanous autoregulatory domain, 90% H2O/10% D2OSample was used to determine resonance assignmentDID_15N_13C_DAD90% H2O/10% D2O
solution5300 uM Diaphanous inhibitory domain, 300 uM [U-100% 15N] Diaphanous autoregulatory domain, 90% H2O/10% D2OSample was used to collect NOE distances for structure calculationDID_15N_DAD90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMDiaphanous inhibitory domain[U-15N]1
500 uMDiaphanous autoregulatory domainnatural abundance1
300 uMDiaphanous inhibitory domain[U-15N]2
500 uMDiaphanous autoregulatory domain[U-13C]2
300 uMDiaphanous inhibitory domain[U-100% 13C; U-100% 15N]3
500 uMDiaphanous autoregulatory domainnatural abundance3
300 uMDiaphanous inhibitory domainnatural abundance4
500 uMDiaphanous autoregulatory domain[U-100% 13C; U-100% 15N]4
300 uMDiaphanous inhibitory domainnatural abundance5
300 uMDiaphanous autoregulatory domain[U-100% 15N]5
Sample conditionsDetails: 20 mM potassium phosphate, 1 mM 4-(2-aminoethyl)benzenesulfonyl fluoride hydrochloride (AEBSF), 0.5 mM ethylenediaminetetraacetic acid (EDTA), 1 mM dithiothreitol (DTT), 100 mM sodium ...Details: 20 mM potassium phosphate, 1 mM 4-(2-aminoethyl)benzenesulfonyl fluoride hydrochloride (AEBSF), 0.5 mM ethylenediaminetetraacetic acid (EDTA), 1 mM dithiothreitol (DTT), 100 mM sodium chloride, 15 mM hexamethylphosphoramide (HMPA), and 10% v/v D2O at pH 7.5 and 305 K
Ionic strength: 140 mM / Label: conditions_1 / pH: 7.5 / Pressure: 1 atm / Temperature: 305 K

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NMR measurement

NMR spectrometerType: Bruker Ascend / Manufacturer: Bruker / Model: Ascend / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
YASARAKriegerrefinement
RefinementMethod: molecular dynamics / Software ordinal: 6
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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